library(dplyr)
library(magrittr)
setClass('ampseq', slots = c(
gt = "ANY",
metadata = "ANY",
markers = "ANY",
loci_performance = "ANY",
pop_summary = "ANY",
controls = "ANY",
discarded_loci = "ANY",
discarded_samples = "ANY",
plots = "ANY"
))
load(params$RData_image)
The haplotype of each sample is stored in the table
aacigar_table within the object
drug_resistant_haplotypes_plot.
plot_relatedness_distribution_between$plot
Figure 1: IBD distribution between sites
plot_frac_highly_related_between$plot
Figure 2: Frequency of highly related among sites
if(!is.na(Variable2)){plot_frac_highly_related_overtime_between$plot_IBD_correlation_matrix}
Figure 2: Frequency of highly related between sites over time
if(!is.na(Variable2)){plot_frac_highly_related_overtime_between$plot_frac_highly_related}
Figure 2: Frequency of highly related between sites over time
IBD_PCA
Figure 3: IBD PCA
qual_col_pals = brewer.pal.info[brewer.pal.info$category == 'qual',]
col_vector = unlist(mapply(brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals)))
set.seed(1)
plot_network(pairwise_relatedness,
threshold = ibd_thres,
metadata = ampseq_object@metadata,
sample_id = 'Sample_id',
group_by = Variable1,
levels = levels(as.factor(ampseq_object@metadata[[Variable1]])),
colors = sample(col_vector, nlevels(as.factor(ampseq_object@metadata[[Variable1]])))
)
Figure 4: IBD network
## $network_object
## IGRAPH 6155350 UN-- 670 8289 --
## + attr: name (v/c)
## + edges from 6155350 (vertex names):
## [1] G4G1103--G4G1050 G4G1103--G4G1153 G4G1103--G4G1649 G4G1103--G4G2071 G4G1103--G4G2268 G4G1103--G4G2471 G4G1103--G4G2567 G4G1103--G4G2938 G4G1103--G4G2999 G4G1103--G4G2872
## [11] G4G1103--G4G3267 G4G1103--MH-212 G4G1106--G4G1458 G4G1106--G4G1193 G4G1106--G4G1342 G4G1106--G4G2583 G4G1106--G4G2612 G4G1106--G4G2487 G4G1106--G4G3159 G4G1106--G4G2786
## [21] G4G1106--MH-273 G4G1106--MP0172 G4G1106--MP0136 G4G1106--MP0031 G4G1106--MP0034 G4G1106--MP0041 G4G1106--MP0093 G4G1106--MP0023 G4G1107--G4G1415 G4G1107--G4G1031
## [31] G4G1050--G4G1107 G4G1153--G4G1107 G4G1107--G4G1198 G4G1342--G4G1107 G4G1107--G4G1607 G4G2268--G4G1107 G4G1107--G4G2396 G4G2471--G4G1107 G4G2567--G4G1107 G4G1107--G4G3143
## [41] G4G1107--G4G2817 G4G2872--G4G1107 G4G3267--G4G1107 G4G1107--G4G3299 G4G1107--G4G3384 G4G1107--MP0016 MP0136 --G4G1107 G4G1107--MP0051 MP0041 --G4G1107 G4G1107--MP0109
## [51] G4G1415--G4G1124 G4G1124--G4G1425 G4G1124--G4G1100 G4G1124--G4G1109 G4G1124--G4G1150 G4G1124--G4G1481 G4G1124--G4G1544 G4G1124--G4G1736 G4G1124--G4G1794 G4G1124--G4G1847
## [61] G4G1124--G4G2143 G4G1124--G4G2145 G4G1124--G4G2459 G4G1124--G4G2306 G4G1124--G4G2652 G4G1124--G4G2688 G4G1124--G4G2728 G4G1124--G4G2976 G4G1124--G4G3126 G4G1124--G4G3402
## [71] G4G1124--G4G3062 G4G1124--G4G3293 G4G1124--G4G3408 G4G1124--MP0144 G4G1124--MP0062 G4G1124--MP0065 G4G1125--G4G1286 G4G1125--G4G1041 G4G1153--G4G1125 G4G1342--G4G1125
## + ... omitted several edges
##
## $plot_network
## NULL